Changeset 2126

Timestamp:

Mar 29, 2006, 2:56:43 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #166 and #167:

• Make IntensityCalculator? an InteractivePlugin?
• Create root bioassayset using other plugins than IntensityCalculator?

Location:

trunk

Files:

• src/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java (modified) (8 diffs)
• www/common/plugin/configure.jsp (modified) (6 diffs)
• www/views/experiments/bioassaysets/create_root_bioassayset.jsp (deleted)
• www/views/experiments/bioassaysets/index.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/list_bioassaysets.jsp (modified) (3 diffs)

trunk/src/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java

@@ -27 +27 @@
 import net.sf.basedb.core.ProgressReporter;
 
+import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.Include;
+import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemParameterType;
+import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.PluginParameter;
+import net.sf.basedb.core.RequestInformation;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.BioAssaySet;
@@ -37 +47 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.AbstractPlugin;
+import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.Plugin;
+import net.sf.basedb.core.plugin.InteractivePlugin;
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.IntensityFormula;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.IntensityCalculator;
 import net.sf.basedb.util.IntensityCalculatorUtil;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 
 /**
-   This plugin provides methods to calculate the intensity for a root bioassayset using different formulas.
-   It needs the following parameters
+   This plugin provides methods to calculate the intensity for a root bioassayset 
+   using different formulas. It needs the following parameters:
 
    <pre>
-   String              : name 
-   Experiment          : experiment
-   List<RawBioAssay>   : rawBioAssays  
-   String              : formula
+   String              : name; The name of the new bioassayset
+   Experiment          : experiment; The experiment we are working on
+   List&gt;RawBioAssay&lt;   : rawBioAssays; The raw bioassays to create bioassays for
+     (must be part of the experiment)
+   Formula             : formula; The formula to use to for calculating intesities
    </pre>
 
-   @author Gregory
+   @author Gregory, Nicklas
+   @version 2.0
+   @base.modified $Date$
 */
 public class IntensityCalculatorPlugin
   extends AbstractPlugin
-  implements Plugin  
+  implements InteractivePlugin 
 {
 
@@ -70 +90 @@
           new AboutImpl
     (
-      "Intensity calculator",
-      "This plugin is used to calculate intensities from raw data creating an initial raw bioassay.",
-      "1.0",
+      "Formula intensity calculator",
+      "This plugin is used to calculate intensities from raw data creating an initial root bioassay set. "+
+      "The intensities are calculated using Formula objects registered for the experiment's raw data type. " +
+      "Thus, the functionality of this plugin can be extended by adding more formula objects to the database.",
+      "2.0",
       "2006, Department of Theoretical Physics, Lund University",
       null,
@@ -79 +101 @@
     );
 
-
+  private static final Set<GuiContext> guiContexts = 
+    Collections.singleton(new GuiContext(Item.BIOASSAYSET, GuiContext.Type.LIST));
+
+  private static final RequestInformation configurePlugin = new RequestInformation
+  (
+    Request.COMMAND_CONFIGURE_PLUGIN,
+    "Configure intensity calculator",
+    "This plugin has no configuration options.",
+    null
+  );
+
+  private static final StringParameterType nameType = 
+    new StringParameterType(BioAssaySet.MAX_NAME_LENGTH, "New bioassayset", true);
+  private static final PluginParameter<String> nameParameter = new PluginParameter<String>(
+    "name", "Bioassay set name", "The name of the root bioassayset", nameType);
+
+  private ItemParameterType<Experiment> experimentType;
+  private PluginParameter<Experiment> experimentParameter;
+
+  private ItemParameterType<RawBioAssay> rawBioAssaysType;
+  private PluginParameter<RawBioAssay> rawBioAssaysParameter;
+
+  private ItemParameterType<Formula> formulaType;
+  private PluginParameter<Formula> formulaParameter;
+
+  private RequestInformation configureJob;
+  
   /**
      Constructor should be empty. 
@@ -86 +134 @@
   {}
   
-
-  /* 
-    Plugin interface implementation 
-    -------------------------------
+  /*
+    From the Plugin interface
+    -------------------------------------------
   */
   public About getAbout()
@@ -95 +142 @@
     return about;
   }
-
-
   /**
      Returns the main plugin type this plugin belongs to.
@@ -106 +151 @@
   }
 
-
-  /**
-     @param request 
-     @param response 
-     @param progress
-  */
   @SuppressWarnings("unchecked")
   public void run(Request request, Response response, ProgressReporter progress)
@@ -118 +157 @@
     try
     {
-      /* name parameter */
+      // name parameter
       String name = (String)job.getValue("name");
   
-      /* experiment parameter*/
-  
-      Integer experimentId = (Integer)job.getValue("experiment_id");
-      if(experimentId != null)
-      {
-        Experiment experiment = Experiment.getById(dc, experimentId.intValue());
-  
-        /* rawBioAssays parameter*/
-        List<RawBioAssay> sources = (List<RawBioAssay>)job.getValues("rawBioAssays");
-        for (RawBioAssay rba : sources)
-        {
-          dc.reattachItem(rba);
-        }
-  
-        /* formula parameter */
-        String formula = (String)job.getValue("formula");
-  
-        /* intensity calculation */
-        RawDataType rdt = experiment.getRawDataType();
-        IntensityFormula intensityFormula = rdt.getIntensityFormula( formula );
-        IntensityCalculator iCalc = IntensityCalculatorUtil.createJepIntensityCalculator(dc, rdt, intensityFormula.getExpressions());
-        int jobId = job.getId();
-        Job thisJob = Job.getById(dc, jobId);
-        BioAssaySet rootBas = IntensityCalculatorUtil.createRootBioAssaySet(dc, experiment, sources, thisJob, iCalc, progress);
-        rootBas.setName(name);
-        Transformation t = rootBas.getTransformation();
-        t.setName(intensityFormula.getTitle());
-        dc.commit();
-        response.setDone("Done");
+      // experiment parameter
+      Experiment experiment = (Experiment)job.getValue("experiment");
+      
+      // To avoid disconnection/reconnection issues
+      experiment = Experiment.getById(dc, experiment.getId());
+  
+      // rawBioAssays parameter
+      List<RawBioAssay> sources = (List<RawBioAssay>)job.getValues("rawBioAssays");
+      for (RawBioAssay rba : sources)
+      {
+        dc.reattachItem(rba);
       }
-      else
-      {
-        response.setError("Experiment id is null", null);
+
+      // Formula parameter
+      Formula formula = (Formula)job.getValue("formula");
+      formula = Formula.getById(dc, formula.getId());
+  
+      // intensity calculation
+      RawDataType rdt = experiment.getRawDataType();
+
+      // IntensityFormula intensityFormula = rdt.getIntensityFormula( formula );
+      IntensityCalculator iCalc = 
+        IntensityCalculatorUtil.createJepIntensityCalculator(dc, rdt, 
+        formula.getFormulas().toArray(new String[formula.getNumFormulas()]));
+      int jobId = job.getId();
+      Job thisJob = Job.getById(dc, jobId);
+
+      BioAssaySet rootBas = IntensityCalculatorUtil.createRootBioAssaySet(dc, experiment, sources, thisJob, iCalc, progress);
+      rootBas.setName(name);
+      Transformation t = rootBas.getTransformation();
+      t.setName(formula.getName());
+      dc.commit();
+      response.setDone("Done");
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+  // -------------------------------------------
+
+  /*
+    From the InteractivePlugin interface
+    -------------------------------------------
+  */
+  public Set<GuiContext> getGuiContexts()
+  {
+    return guiContexts;
+  }
+  /**
+    Always false, since plugin doesn't operate on individual items.
+  */
+  public boolean isInContext(GuiContext context, Object item)
+  {
+    return false;
+  }
+  /**
+    The {@link Request#COMMAND_CONFIGURE_PLUGIN} command will not ask for
+    any parameters.
+    The {@link Request#COMMAND_CONFIGURE_JOB} command will ask for
+    the parameters mentioned in the class documentation.
+  */
+  public RequestInformation getRequestInformation(GuiContext context, String command)
+    throws BaseException
+  {
+    RequestInformation requestInformation = null;
+    if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+    {
+      requestInformation = configurePlugin;
+    }
+    else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+    {
+      requestInformation = getConfigureJobParameters();
+    }
+    return requestInformation;
+  }
+  /**
+    Store configuration settings for {@link Request#COMMAND_CONFIGURE_PLUGIN}, 
+    and {@link Request#COMMAND_CONFIGURE_JOB}.
+  */
+  @SuppressWarnings("unchecked")
+  public void configure(GuiContext context, Request request, Response response)
+  {
+    String command = request.getCommand();
+    
+    try
+    {
+      if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+      {
+        response.setDone("No configuration needed.");
       }
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-  }
+      else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+      {
+        List<Throwable> errors = validateRequestParameters(configureJob.getParameters(), request);
+        if (errors != null)
+        {
+          response.setError(errors.size()+" invalid parameter(s) were found in the request", errors);
+          return;
+        }
+        
+        Experiment experiment = (Experiment)request.getParameterValue("experiment");
+        DbControl dc = sc.newDbControl();
+        int numSpots = 0;
+        try
+        {
+          experiment = Experiment.getById(dc, experiment.getId());
+          List<RawBioAssay> rawBioAssays = (List<RawBioAssay>)request.getParameterValues("rawBioAssays");
+          for (RawBioAssay rba : rawBioAssays)
+          {
+            if (!experiment.isUsing(rba))
+            {
+              throw new InvalidDataException("Raw bioassay '" + rba.getName() + 
+                "' is not part of the experiment '" + experiment.getName()+"'");
+            }
+            numSpots += rba.getSpots();
+          }
+        }
+        finally
+        {
+          if (dc != null) dc.close();
+        }
+        
+        Formula formula = (Formula)request.getParameterValue("formula");
+        if (formula.getFormulaType() != Formula.Type.INTENSITY_EXPRESSION)
+        {
+          throw new InvalidDataException("The selected formula is not an intensity expression formula: " + 
+            formula.getName());
+        }
+        if (formula.getRawDataType() != experiment.getRawDataType())
+        {
+          throw new InvalidDataException("The selected formula '"+formula.getName()+
+            "' uses a different raw data type than the experiment '" + experiment.getName()+"'");
+        }
+        
+        storeValue(job, request, nameParameter);
+        storeValue(job, request, experimentParameter);
+        storeValues(job, request, rawBioAssaysParameter);
+        storeValue(job, request, formulaParameter);
+        
+        Job.ExecutionTime execTime = Job.ExecutionTime.SHORT;
+        // TODO - this should be configurable in some way
+        if (numSpots > 1000000 && numSpots < 10000000)
+        {
+          execTime = Job.ExecutionTime.MEDIUM;
+        }
+        else
+        {
+          execTime = Job.ExecutionTime.LONG;
+        }
+        
+        response.setDone("Job configuration complete", execTime);
+      }
+    }
+    catch (Throwable ex)
+    {
+      response.setError(ex.getMessage(), Arrays.asList(ex));
+      ex.printStackTrace();
+    }
+  }
+
+  
+  private RequestInformation getConfigureJobParameters()
+  {
+    if (configureJob == null)
+    {
+      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
+      
+      experimentType = new ItemParameterType<Experiment>(Experiment.class, null, true, 1, null);
+      experimentParameter = new PluginParameter<Experiment>(
+        "experiment", "Experiment", "The experiment we are working with", experimentType);
+      
+      parameters.add(experimentParameter);
+      parameters.add(nameParameter);
+      
+      DbControl dc = sc.newDbControl();
+      try
+      {
+        int experimentId = sc.getCurrentContext(Item.EXPERIMENT).getId();
+        Experiment experiment = Experiment.getById(dc, experimentId);
+        
+        ItemQuery<RawBioAssay> rawBioAssayQuery = experiment.getRawBioAssays();
+        rawBioAssayQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+        rawBioAssayQuery.order(Orders.asc(Hql.property("name")));
+        List<RawBioAssay> rawBioAssays = new ArrayList<RawBioAssay>(rawBioAssayQuery.list(dc));
+        rawBioAssaysType = new ItemParameterType<RawBioAssay>(RawBioAssay.class, null, true, 0, rawBioAssays);
+        rawBioAssaysParameter = new PluginParameter<RawBioAssay>(
+          "rawBioAssays", "Raw bioassays", "Select the raw bioassays to use when creating the root bioassay set",
+          rawBioAssaysType);
+        
+        parameters.add(rawBioAssaysParameter);
+        
+        ItemQuery<Formula> formulaQuery = Formula.getQuery(Formula.Type.INTENSITY_EXPRESSION, 
+            experiment.getRawDataType());
+        formulaQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+        formulaQuery.order(Orders.asc(Hql.property("name")));
+        List<Formula> formulas = new ArrayList<Formula>(formulaQuery.list(dc));
+        formulaType = new ItemParameterType<Formula>(Formula.class, null, true, 1, formulas);
+        formulaParameter = new PluginParameter<Formula>(
+          "formula", "Formula", "Select the expression to use for calculating the intensities",
+          formulaType);
+        parameters.add(formulaParameter);
+      }
+      finally
+      {
+        if (dc != null) dc.close();
+      }     
+      configureJob = new RequestInformation
+      (
+        Request.COMMAND_CONFIGURE_JOB,
+        "Intensity calculation options",
+        "Select which raw bioassays to use and a formula for the calculations",
+        parameters
+      );
+    }
+    return configureJob;
+  }
+
 }

trunk/www/common/plugin/configure.jsp

@@ -129 +129 @@
             }
             // Finally we use the parameters default value
-            if (values == null || values.size() == 0)
+            if ((values == null || values.size() == 0) && pType.getDefaultValue() != null)
             {
               values = Collections.singletonList(pType.getDefaultValue());
@@ -579 +579 @@
                   {
                     %>
-                    <select name="<%=inputName%>" multiple size="10"
+                    <select name="<%=inputName%>" multiple size="10" style="width: 30em;"
                       onchange="setEnumValues('<%=inputName%>')">
                     <%
@@ -587 +587 @@
                     String listValue = "";
                     String listText = "";
+                    String listTitle = "";
                     if (value instanceof Date) 
                     {
@@ -596 +597 @@
                       BasicItem item = (BasicItem)value;
                       listValue = Integer.toString(item.getId());
-                      listText = HTML.encodeTags(item instanceof Nameable ? ((Nameable)item).getName() : item.toString());
+                      if (item instanceof Nameable)
+                      {
+                        Nameable nameable = (Nameable)item;
+                        listText = HTML.encodeTags(nameable.getName());
+                        listTitle = HTML.encodeTags(nameable.getDescription());
+                      }
+                      else
+                      {
+                        listText = item.toString();
+                      }
                     }
                     else
@@ -604 +614 @@
                     }
                     %>
-                    <option value="<%=listValue%>"><%=listText%>
+                    <option value="<%=listValue%>" title="<%=listTitle%>"><%=listText%>
                     <%
                   }
@@ -786 +796 @@
                   if (cc.getId() != 0)
                   {
+                    BasicItem item = parameterItemType.getById(dc, cc.getId());
+                    String display = "";
+                    if (item instanceof Nameable)
+                    {
+                      Nameable nameable = (Nameable)item;
+                      display = nameable.getName();
+                    }
+                    else 
+                    {
+                      display = item.toString();
+                    }
                     %>
-                    <%=parameterItemType.getById(dc, cc.getId()).toString()%>
+                    <b><%=HTML.encodeTags(param.getLabel())%></b><br>
+                    <input class="text disabled" size="50" type="text" disabled value="<%=HTML.encodeTags(display)%>">
                     <%
                   }

trunk/www/views/experiments/bioassaysets/index.jsp

@@ -83 +83 @@
 final String viewPage = "view_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
 final String editPage = "edit_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
-final String newPage = "create_root_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
+
+final String newPage = "../../../common/plugin/index.jsp?ID="+ID
+  +"&cmd=SelectPlugin&main_type=INTENSITY&item_type=BIOASSAYSET&context_type=LIST&title=Create+root+bioassay+set";
+
 sc.getCurrentContext(Item.EXPERIMENT).setId(experimentId);
 

trunk/www/views/experiments/bioassaysets/list_bioassaysets.jsp

@@ -166 +166 @@
     function newItem()
     {
-      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 600, 400);
+      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 740, 540);
     }
     function editItem(itemId)
@@ -210 +210 @@
     function runPlugin(cmd)
     {
-      Table.submitToPopup(formId, cmd, 540, 460);
+      Table.submitToPopup(formId, cmd, 740, 540);
     }
     function returnSelected()
@@ -455 +455 @@
           title="New root bioassay set&hellip;" 
           tooltip="<%=createPermission ? "Create new event" : "You do not have permission to create events"%>" 
+          visible="<%=pluginCount.containsKey(Plugin.MainType.INTENSITY)%>"
         />
         <tbl:button